Sequence
atgc intronic sequence ATGC exonic sequence...ctagaaattgagattttccagacttttcttctattaatttcagcctaatcttgagcaatgagacattgagtaatttttttccttttcctgcacactgcagATGGTCGCAGATTGCGACGCAGCTTCCCGGTCGCACTGACAACGAAATAAAGAACTTCTGGAATTCCTGTATTAAGAAGAAGTTACGCAACATCGGTATT
Basic information
species | Physcomitrella patens |
transcript | PP1S24_48V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S24_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g36460.1 (Oryza sativa), 3'ss of exon 2
-ctagaaattgagattttccagacttttcttctattaatttcagcctaatcttgagcaatgagacattgagtaatttttttccttttcctgcacactg--cagATGGTCGCAGATTGCGACGCAGCTTCCCGGTCGCACTGACAACGAAATAAAGAACTTCTGGAATTCCTGTATTAAGAAGAAGTTACGCAACATCGGTATT
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cgcatgagctgatagtgcc--gttttggctaccgaaatgttgttacgagagtctgacaacacgatcccaa-tgtttgcacatggatttgtgaattgtgatcagGTGGTCCCAGATTGCGGCGCAGCTGCCCGGCCGGACGGACAACGAGATCAAGAACTTCTGGAACTCGTGCCTCAAGAAGAAGCTCCGGCAGCGCGGCATC
upper sequence: PP1S24_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA01G43120.1 (Glycine max), 3'ss of exon 2
ctagaaattgagattttccagacttttcttctattaatttcagcctaatcttgagcaatgagacattgagtaattt-ttttccttttcctgcacactgcagATGGTCGCAGATTGCGACGCAGCTTCCCGGTCGCACTGACAACGAAATAAAGAACTTCTGGAATTCCTGTATTAAGAAGAAG-TTACGCAACATCGGTATT
| |||| ||| | | | ||| || | | || | || || | | | | | | | | | | || | | ||||| | || | ||||||||| | || ||||| | || | || ||| | |||||||||||||||||||||| ||||||||| || || || ||||| ||| | | | |
-tcttaattaagaagatactgtttttcattatttaaacattagaatatacatacgtactcaattaattaattatatatgttcctgtgtttgagaaatgcagATGGGCTCACATTGCAAGCCACTTACCAGGTAGAACTGACAACGAAATAAAGAACTACTGGAATTCTTGGATCAAAAAGAAAATTAGAAAGCCTTCTTCG-
upper sequence: PP1S24_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G57560.1 (Arabidopsis thaliana), 3'ss of exon 2
ctagaaattgagattttccagacttttcttctattaatttcagcctaatcttgagcaatgagacattgagtaatttttttccttttcctgcacactgcagATGGTCGCAGATTGCGACGCAGCTTCCCGGTCGCACTGACAACGAAATAAAGAACTTCTGGAATTCCTGTATTAAGAAGAAGTTACGCAACATCGGTATT
| || | | | |||| | || | | ||| || ||| | | | || || || | |||||||||||| ||||| || ||||||||| | || |||||||| ||||||||||| |||||||| || |||||||||||| | || | || |||
--------------gtaacaatcacaattacaattattctctgttt----ctga--aacagagtattttctgaaatcccctgttatcttgtat----cagATGGTCGCAAATTGCTGCGAGGCTTCCCGGGAGAACCGACAACGAGATAAAGAACTTGTGGAATTCGTGCATTAAGAAGAAGCTGATGAAGAAAGGCATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatcttgagcaatgagacattgagtaatttttttccttttcctgcacactgcagATGGTCGCAGATTGCGACGCAGCTTCCCGGTCGCACTGACAACGAAATAAAGAACTTCTGGAATTCCTGTATTAAGAAGAAGTTACGCAACATCGGTATT
gcctaat putative branch site (score: 3)
tttttttccttttcct putative PPT
attgagtaattttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagaaattgagattttccagacttttcttctattaatttcagcctaatcttgagcaatgagacattgagtaatttttttccttttcctgcacactgcagATGGTCGCAGATTGCGACGCAGCTTCCCGGTCGCACTGACAACGAAATAAAGAACTTCTGGAATTCCTGTATTAAGAAGAAGTTACGCAACATCGGTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT